@include "rna/_sc_vdj_assembler_stages.mro"

call REPORT_CONTIGS(
    vdj_reference_path = "/scratch/etanis/ST-118/references/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0",
    cell_barcodes      = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/cell_barcodes.json",
    contigs            = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/contig_fasta.fasta",
    annotations        = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/HANDLE_NO_VDJ_REF/fork0/chnk0-ucc6a7a7cd8/files/all_contig_annotations.json",
    filter_summary     = null,
    contig_summary     = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/summary_tsv.tsv",
    umi_summary        = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/umi_summary_tsv.tsv",
)
